"I'll pray for you"
"Will you? I'll tell my rainbow hedgehog unicorn about you too, oh sorry he doesn't exist...either."

I thank them for their interest and concern. But never for the prayers.

I used to be deeply offended whenever I came to someone with a problem and they said that they would pray for me. To me, an atheist at the time, the gesture seemed empty. I didn't understand why that's all they could do.
A few years ago, however, I realized why I shouldn't be offended by these words. To someone who believes in God, and believes in the power of prayer, that is the most meaningful thing they can do for you. There is no condescension whatsoever, although it can sound like that sometimes. They just want you to know that they care about you deeply, and that they are asking God -- an entity which they believe can fix all problems -- to be there for you. It doesn't make sense to people who don't believe in a higher power, and that is understandable. But (in my opinion) there is no reason to be offended when someone is giving you their love, and an "I'll pray for you" is best met with a "Thank you," whether you agree with it completely or not

I say thank you for thinking of me. It's something I just kinda ignore.

"Thank you, I need all the help I can get" with just a pinch of humor and sarcasm full in the knowledge that their prayers are really for their own benefit.

Personally I find them to be somewhat condescending when they say that to me.
One of my numerous responses to them is " Is not praying simply like trying to swim in dry, desert sand?"

I thank them for the kind thoughts. It is usually how the people around me tell me they are hoping for the best.

I like the old "You'll pray for me? Then I guess I'll have to think for you." response.

I tell them, "Don't bother, prayers have been demonstrated to not be effective and I don't believe in such silly superstitions."

It depends if you want to be actively 'anti-theist'. If not, react as if they had just said 'good luck, hope things go well'... which is basically that they are saying. If you want to make a point, you can go for something like 'Thank you - and I'll talk to my pet gerbil for you. I expect similar results.'

They are condescending. I just blow the fools off and go on with my life.

"I will think for you"

Me: "Well, if it makes you feel any better, have at it, toots."

I really have never felt that people who say they will pray for me are being condescending. People who say that for the most part do it out of a sense of compassion and a belief that they are being helpful. My response is, thanks! The people who who describe such people as "fools" are the one who are condescending.

It depends on their purpose for saying it. If they intend to influence your decisions contrary to your intent then i don't appreciate it. If they are simply trying to help me then i appreciate it but i know it's not beneficial. Even if their naive you shouldn't respond to kindness with anger

Nod and smile. I have no interest in challenging their beliefs, nor having them challenge mine.

Ask them not to and tell them it doesn't work

I say “I wish you all the best too” and leave it at that. No interest in creating a conflict or a long drawn out situation.

It really depends on who it is from, those that don't know my "beliefs" I take it as a nice gesture and those that know I take it as an insult

I just smile and nod. Some of my friends will say thank you but I see no reason to extend gratitude. I find it a shallow and meaningless gesture.

You could just say "Thank you for your thoughts". Polite way to get your point across.

They are trying to be nice, I just let it slide.

You say thanks and go on with your dailies.

Thanks. I'll take all the best wishes I can get.

I agree. I mean, I get that they mean well, but at the same time, it definitely seems condescending. I just always say "Trust me, my mom has been praying for me my entire life. Must be a lost cause" Then you smile and walk away. Lol my little way of holding back